Shark nurseries | Data Wrangling
For each of our modules we will have a project-folder with an Rproject, *.qmd-files, and sub-directories for data, scripts, and results as described in our Rproject Tutorial. You should create a directory on your Desktop or Documents folder on your laptop (name it something like bi349) as a home directory for all of our project folders this semester.
Download the 01_SharkNurseries project folder. Once you have downloaded it, unzip the project directory into your bi349 directory1.
1 On a MacOS it will automatically unzip the folder for you, you should be able to directly move the entire unzipped directory to your bi349 folder. On a Windows OS you will need to right click and select extract all you can generally specifiy which directory you want to unzip your file into.
Once you have done this, you can open the Rproj for this module either by double clicking on it which will launch Rstudio or by opening Rstudio and then using File > Open Project or by clicking on the Rproject icon in the top right of your program window and selecting Open Project.
Once you have opened a project you should see the project name in the top right corner2.
2 Pro tip: If you run into issues where a quarto document won’t render or file paths aren’t working (especially if things were working previously) one of your first steps should be to double check that the correct Rproj is loaded.
Essential fish habitat: Shark Nurseries
The Magnuson-Stevens Act (1996) defined essential fish habitat as “those waters and substrate necessary to fish for spawning, breeding, feeding or growth to maturity”, i.e. they are habitats necessary for an organism to complete their life cycle. Identifying essential fish habitats is critical for management and conservation plans because it enables policy makers to prioritize certain ecosystems.
While some elasmobranchs (sharks, rays, skates) inhabit estuaries year round, many use the estuaries for specific purposes such as feeding, mating, gestation, parturition or as nurseries and only inhabit them during specific life history stages. Estuaries are heavily impacted by humans - overfishing, pollution, habitat destruction and altered flow regimes all affect the biological communities they support.
Broadly, shark nurseries are areas where young are born and/or reside in during maturation. Typically, these would areas that provide additional protection (e.g. mangroves for hiding) and plenty of food.
Shark Nurseries have three defining criteria(Heupel et al. 2018; Heupel, Carlson, and Simpfendorfer 2007):
- an area where sharks are more commonly encountered within compared to outside of.
- an area in which Young-of-the-year (YOY)/juveniles remain in or return to for extended periods of time.
- an area that is repeatedly used across years.
Identifying shark nurseries on the Texas Coast
Texas Parks and Wildlife (TPWD) defines eight major estuaries along the Texas coastline and performs regular shore-based gill net surveys for 10 week periods in April - June and September to November.
Analysis of this survey has identify eight elasmobranch species present in these ecosystems (Plumlee et al. 2018):
- Bull shark
- Bonnethead
- Cownose ray
- Blacktip shark
- Atlantic stingray
- Atlantic sharpnose shark
- Spinner shark
- Scalloped hammerhead
- Finetooth shark
- Lemon shark
Gill nets generally exclude individuals > 2m.
More recently, a multi-year open water long-lining study targeting elasmobranchs was performed in three estuarine locations near Corpus Christi, TX that are considered putative shark nurseries. Here, the sampling period lasted from May to November (Swift and Portnoy 2021).
This study wanted to answer four questions to further understand whether these locations should be considered shark nurseries and therefore as essential fish habitat for specific elasmobranch species.
- How does the composition of elasmobranch communities compare across sites?
- How does the catch-per-unit-effort (CPUE) per species and life history compare across sites?
- What do the sex ratios look like?
- What environmental predictors can we use to predict presence of elasmobranchs?
In this module we will interact with the data set generated for this study to learn how to wrangle data sets using R in the tidyverse and then we will apply those skills to answer these questions.